La divina substancia como māsūra y muftaraqa. Un intento de reinterpretación de la terminología trinitaria de acuerdo con la enseñanza de al-Risāla fī l-thālūth al-muqaddas de Abū Rā’iṭa

The paper deals with Abū Rāi’ṭa’s Trinitarian terminology found in his al-Risāla fī l-thālūth al-muqaddas. In particular, it concentrates on an expression that epitomises the unity of the divine substance and multiplicity of hypostaseis, i.e. “māsūra and muftaraqa”. In the light of the Abū Rāi’ṭa’s understanding of the the Trinitarian doctrine, an attempt of reinterpretation of the meaning of these key-terms is presented.Este artículo trata de la terminología trinitaria de Abū Rā’iṭa contenida en su al-Risāla fi l-thālūth al-muqaddas. Concretamente, se centra en una expresión que simboliza la unidad de la sustancia divina y la multiplicidad de hipóstasis, es decir “māsūra y muftaraqa”. Ofrecemos un intento de reinterpretación del significado de estos términos clave de acuerdo con la comprensión de la doctrina trinitaria de Abū Rā’iṭa

Relativistic slim disks with vertical structure

We report on a scheme for incorporating vertical radiative energy transport into a fully relativistic, Kerr-metric model of optically thick, advective, transonic alpha disks. Our code couples the radial and vertical equations of the accretion disk. The flux was computed in the diffusion approximation, and convection is included in the mixing-length approximation. We present the detailed structure of this "two-dimensional" slim-disk model for alpha=0.01. We then calculated the emergent spectra integrated over the disk surface. The values of surface density, radial velocity, and the photospheric height for these models differ by 20%-30% from those obtained in the polytropic, height-averaged slim disk model considered previously. However, the emission profiles and the resulting spectra are quite similar for both types of models. The effective optical depth of the slim disk becomes lower than unity for high values of the alpha parameter and for high accretion rates.Comment: 15 pages, 18 figures (2 new), A&A in pres

Spatial chromatin architecture alteration by structural variations in human genomes at the population scale.

BACKGROUND: The number of reported examples of chromatin architecture alterations involved in the regulation of gene transcription and in disease is increasing. However, no genome-wide testing has been performed to assess the abundance of these events and their importance relative to other factors affecting genome regulation. This is particularly interesting given that a vast majority of genetic variations identified in association studies are located outside coding sequences. This study attempts to address this lack by analyzing the impact on chromatin spatial organization of genetic variants identified in individuals from 26 human populations and in genome-wide association studies. RESULTS: We assess the tendency of structural variants to accumulate in spatially interacting genomic segments and design an algorithm to model chromatin conformational changes caused by structural variations. We show that differential gene transcription is closely linked to the variation in chromatin interaction networks mediated by RNA polymerase II. We also demonstrate that CTCF-mediated interactions are well conserved across populations, but enriched with disease-associated SNPs. Moreover, we find boundaries of topological domains as relatively frequent targets of duplications, which suggest that these duplications can be an important evolutionary mechanism of genome spatial organization. CONCLUSIONS: This study assesses the critical impact of genetic variants on the higher-order organization of chromatin folding and provides insight into the mechanisms regulating gene transcription at the population scale, of which local arrangement of chromatin loops seems to be the most significant. It provides the first insight into the variability of the human 3D genome at the population scale

3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome.

Structural variants (SVs) that alter DNA sequence emerge as a driving force involved in the reorganisation of DNA spatial folding, thus affecting gene transcription. In this work, we describe an improved version of our integrated web service for structural modeling of three-dimensional genome (3D-GNOME), which now incorporates all types of SVs to model changes to the reference 3D conformation of chromatin. In 3D-GNOME 2.0, the default reference 3D genome structure is generated using ChIA-PET data from the GM12878 cell line and SVs data are sourced from the population-scale catalogue of SVs identified by the 1000 Genomes Consortium. However, users may also submit their own structural data to set a customized reference genome structure, and/or a custom input list of SVs. 3D-GNOME 2.0 provides novel tools to inspect, visualize and compare 3D models for regions that differ in terms of their linear genomic sequence. Contact diagrams are displayed to compare the reference 3D structure with the one altered by SVs. In our opinion, 3D-GNOME 2.0 is a unique online tool for modeling and analyzing conformational changes to the human genome induced by SVs across populations. It can be freely accessed at https://3dgnome.cent.uw.edu.pl/

Testing slim-disk models on the thermal spectra of LMC X-3

Slim-disk models describe accretion flows at high luminosities, while reducing to the standard thin disk form in the low luminosity limit. We have developed a new spectral model, slimbb, within the framework of XSPEC, which describes fully relativistic slim-disk accretion and includes photon ray-tracing that starts from the disk photosphere, rather than the equatorial plane. We demonstrate the features of this model by applying it to RXTE spectra of the persistent black-hole X-ray binary LMC X-3. LMC X-3 has the virtues of exhibiting large intensity variations while maintaining itself in soft spectral states which are well described using accretion-disk models, making it an ideal candidate to test the aptness of slimbb. Our results demonstrate consistency between the low-luminosity (thin-disk) and high luminosity (slim-disk) regimes. We also show that X-ray continuum-fitting in the high accretion rate regime can powerfully test black-hole accretion disk models.Comment: 6 pages, 5 figures, submitted to A&

Double Compact Objects I: The Significance Of The Common Envelope On Merger Rates

The last decade of observational and theoretical developments in stellar and binary evolution provides an opportunity to incorporate major improvements to the predictions from populations synthesis models. We compute the Galactic merger rates for NS-NS, BH-NS, and BH-BH mergers with the StarTrack code. The most important revisions include: updated wind mass loss rates (allowing for stellar mass black holes up to 80 \msun), a realistic treatment of the common envelope phase (a process that can affect merger rates by 2--3 orders of magnitude), and a qualitatively new neutron star/black hole mass distribution (consistent with the observed "mass gap"). Our findings include: (i) The binding energy of the envelope plays a pivotal role in determining whether a binary merges within a Hubble time. (ii) Our description of natal kicks from supernovae plays an important role, especially for the formation of BH-BH systems. (iii) The masses of BH-BH systems can be substantially increased in the case of low metallicities or weak winds. (iv) Certain combinations of parameters underpredict the Galactic NS-NS merger rate, and can be ruled out. {\em (v)} Models incorporating delayed supernovae do not agree with the observed NS/BH "mass gap", in accordance with our previous work. This is the first in a series of three papers. The second paper will study the merger rates of double compact objects as a function of redshift, star formation rate, and metallicity. In the third paper we will present the detection rates for gravitational wave observatories, using up-to-date signal waveforms and sensitivity curves.Comment: 41 pages, 20 figures, accepted for ApJ & new model

Whole Transcriptome Sequencing Reveals Gene Expression and Splicing Differences in Brain Regions Affected by Alzheimer's Disease

Recent studies strongly indicate that aberrations in the control of gene expression might contribute to the initiation and progression of Alzheimer's disease (AD). In particular, alternative splicing has been suggested to play a role in spontaneous cases of AD. Previous transcriptome profiling of AD models and patient samples using microarrays delivered conflicting results. This study provides, for the first time, transcriptomic analysis for distinct regions of the AD brain using RNA-Seq next-generation sequencing technology. Illumina RNA-Seq analysis was used to survey transcriptome profiles from total brain, frontal and temporal lobe of healthy and AD post-mortem tissue. We quantified gene expression levels, splicing isoforms and alternative transcript start sites. Gene Ontology term enrichment analysis revealed an overrepresentation of genes associated with a neuron's cytological structure and synapse function in AD brain samples. Analysis of the temporal lobe with the Cufflinks tool revealed that transcriptional isoforms of the apolipoprotein E gene, APOE-001, -002 and -005, are under the control of different promoters in normal and AD brain tissue. We also observed differing expression levels of APOE-001 and -002 splice variants in the AD temporal lobe. Our results indicate that alternative splicing and promoter usage of the APOE gene in AD brain tissue might reflect the progression of neurodegeneration